Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases
Abstract Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30–40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-11-01
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| Series: | npj Genomic Medicine |
| Online Access: | https://doi.org/10.1038/s41525-021-00261-1 |
| _version_ | 1819006922844536832 |
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| author | Zeinab Fadaie Laura Whelan Tamar Ben-Yosef Adrian Dockery Zelia Corradi Christian Gilissen Lonneke Haer-Wigman Jordi Corominas Galuh D. N. Astuti Laura de Rooij L. Ingeborgh van den Born Caroline C. W. Klaver Carel B. Hoyng Niamh Wynne Emma S. Duignan Paul F. Kenna Frans P. M. Cremers G. Jane Farrar Susanne Roosing |
| author_facet | Zeinab Fadaie Laura Whelan Tamar Ben-Yosef Adrian Dockery Zelia Corradi Christian Gilissen Lonneke Haer-Wigman Jordi Corominas Galuh D. N. Astuti Laura de Rooij L. Ingeborgh van den Born Caroline C. W. Klaver Carel B. Hoyng Niamh Wynne Emma S. Duignan Paul F. Kenna Frans P. M. Cremers G. Jane Farrar Susanne Roosing |
| author_sort | Zeinab Fadaie |
| collection | DOAJ |
| description | Abstract Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30–40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7, CEP78, EYS, FAM161A, and HGSNAT. Gene disrupting structural variants were also detected in ATXN7, PRPF31, and RPGRIP1. In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants. |
| first_indexed | 2024-12-21T00:16:23Z |
| format | Article |
| id | doaj.art-134ff20611604419a17d57355443d530 |
| institution | Directory Open Access Journal |
| issn | 2056-7944 |
| language | English |
| last_indexed | 2024-12-21T00:16:23Z |
| publishDate | 2021-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Genomic Medicine |
| spelling | doaj.art-134ff20611604419a17d57355443d5302022-12-21T19:22:13ZengNature Portfolionpj Genomic Medicine2056-79442021-11-016111110.1038/s41525-021-00261-1Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseasesZeinab Fadaie0Laura Whelan1Tamar Ben-Yosef2Adrian Dockery3Zelia Corradi4Christian Gilissen5Lonneke Haer-Wigman6Jordi Corominas7Galuh D. N. Astuti8Laura de Rooij9L. Ingeborgh van den Born10Caroline C. W. Klaver11Carel B. Hoyng12Niamh Wynne13Emma S. Duignan14Paul F. Kenna15Frans P. M. Cremers16G. Jane Farrar17Susanne Roosing18Department of Human Genetics, Radboud University Medical CenterThe School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College DublinRappaport Faculty of Medicine, Technion-Israel Institute of TechnologyThe School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College DublinDepartment of Human Genetics, Radboud University Medical CenterDepartment of Human Genetics, Radboud University Medical CenterDepartment of Human Genetics, Radboud University Medical CenterDepartment of Human Genetics, Radboud University Medical CenterDepartment of Human Genetics, Radboud University Medical CenterDepartment of Human Genetics, Radboud University Medical CenterThe Rotterdam Eye HospitalDepartment of Ophthalmology, Erasmus Medical CenterDonders Institute for Brain, Cognition and Behavior, Radboud University Medical CenterDepartment of Ophthalmology, Royal Victoria Eye and Ear HospitalDepartment of Ophthalmology, Royal Victoria Eye and Ear HospitalThe School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College DublinDepartment of Human Genetics, Radboud University Medical CenterThe School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College DublinDepartment of Human Genetics, Radboud University Medical CenterAbstract Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30–40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7, CEP78, EYS, FAM161A, and HGSNAT. Gene disrupting structural variants were also detected in ATXN7, PRPF31, and RPGRIP1. In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants.https://doi.org/10.1038/s41525-021-00261-1 |
| spellingShingle | Zeinab Fadaie Laura Whelan Tamar Ben-Yosef Adrian Dockery Zelia Corradi Christian Gilissen Lonneke Haer-Wigman Jordi Corominas Galuh D. N. Astuti Laura de Rooij L. Ingeborgh van den Born Caroline C. W. Klaver Carel B. Hoyng Niamh Wynne Emma S. Duignan Paul F. Kenna Frans P. M. Cremers G. Jane Farrar Susanne Roosing Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases npj Genomic Medicine |
| title | Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases |
| title_full | Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases |
| title_fullStr | Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases |
| title_full_unstemmed | Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases |
| title_short | Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases |
| title_sort | whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases |
| url | https://doi.org/10.1038/s41525-021-00261-1 |
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